Participation and compliance are critical to the success of any large-scale study of canine disease using DNA markers. Most canine genetic studies rely upon DNA extracted from peripheral blood samples. We assessed the utility of buccal swab epithelial cells and toe nails as a source of DNA for use in genomic screening studies. Using eight multiplexed canine microsatellite markers, amplified DNA obtained from peripheral blood, and from freshly extracted buccal epithelial cells, and buccal swab DNA extracted and stored at 20 degrees C for 27 months or extracted from toe nails were compared for three dogs. The accuracy of the genotyping at each locus was identical for each preparation. Buccal swab DNA samples were readily and uniformly amplified and could be stored for years without loss of integrity. Each buccal swab provided sufficient DNA for more than 200 individual PCR reactions. Toe nails provided ample DNA for thousands of PCR reactions and had the added advantage of ease of storage of the original tissues. These studies demonstrate the potential utility of DNA derived from buccal swabs or nails in large-scale genomic scanning and marker linkage studies.